I carry two bags when I fly--one on wheels, that carries my computer, my medicines, good jewelry, backup travel documents, and usually a change of clothes (chances are I have to look presentable when I get off the flight). That stuff I don't touch until I get off the plane. The stuff I need with me during my flight I separate and keep in my purse, which stays beside me.
First, get a good bag. I've taken more than thirty five flights in the past two years, about half being transatlantic, and I have found two that really hold up, no matter what you do to them. The first is Vera Bradley's "The Vera", an oversized tote bag with six inside pockets (huge) and two outside pockets, including one pocket that zips closed. It's spacious and hold everything and keeps it separated. Done. The second is Baggallini's "A La Carte Bagg", which doesn't have as much space, but has six pockets OUTSIDE, and really detailed organization inside. Fantastic. Both are roughly eighty dollars, and they can really handle a lot of wear and tear.
Pack food. I hate airline food (and it's usually overly salty, which you want to avoid when flying) so I pack plain sandwiches on fibrous bread (sans condiments) and usually Fiber One bars--possibly a sweet snack if it's a long flight. Also, the second you pass security, buy as much water as you feel physically comfortable carrying--keeping properly hydrated REDUCES JET LAG and LESSENS THE DEHYDRATION OF FLYING.
Next up, entertainment. One book, one iPod, one trashy magazine: this is my recipe for bliss. I load my iPod up with more than I am physically able to watch or listen to in one sitting, and keep it accessible; even if you're not actually listening to anything, keeping those little white earbuds in is the single best way to avoid the awkward overtalker in the middle seat.
About half way through the flight, I get up, walk around, and have a little mini toilette. I like to wash my face (so keep facial wipes handy! They're less mess than actual face wash, and *bonus* you can do it at your seat) reapply moisturizer (absolutely key. Skin is prone to overdrying on planes, which increases oil production and BANG! Breakout when you want it least) and brush my teeth.
As you're about to land, if you have somewhere to be or someone to see, throw on the absolute basics--a little eye gel, mascara, and maybe a light touch of foundation. That's it. Keep it simple, and you'll stay fresh and comfortable all flight long!